Comparative analysis of CRISPR-Cas systems of Yersinia pestis and Escherichia coli strains
Author(s): Eze Uchenna Nwabunwanne, Ifekthar Bin Naser, Olunuga Omotola, Ubenyi Stanley Mary and Ugwu Chukwuebuka V
Abstract: The CRISPR-Cas system primarily refers to the clustered regularly interspaced short palindromic repeats (CRISPR) and its related protein enzymes (Cas) that confer adaptive protection against bacteriophages and other exogenous elements. The CRISPR-spacers that constitute the CRISPR-Cas systems have been reportedly found in Prokaryotes and Archea. This study analyzed and compared genome assemblies of E. coli and Yersinia pestis with the aid of bioinformatics tools (MinCED, MUSCLE alignment tool, nucleotide Basic Local Alignment Search tool (nBLAST), and prokaryotic database of the National Centre for Biotechnology Information (NCBI). The CRISPR-spacer analyses of meta-genomic sequences of 162 Escherichia coli and 121 Yersinia pestis strains showed the presence of 4 CRISPR classes (I, II, III, and IV) in E. coli and 3 CRISPR classes (I, II, and III) in Y. pestis, respectively. The result of MinCED-CRISPR analysis of CRISPR size of genome assemblies of E. coli and Y. pestis strains showed that E. coli CRISPR class I had the highest percentage value (51.9%) compared with E. coli class II (42%), Y. pestis CRISPR class I (40%), Y. pestis CRISPR class II (36%), Y. pestis CRISPR class III (24%), E. coliISPR class class III (4.8%) and E. coli class IV (1%). It further revealed that no CRISPR sequences were found in class IV of Y. pestis strains. The result of CRISPR-spacer contents also showed that the E. coli CRISPR class I showed the highest significant percentage value (54.6%) than Y. pestis CRISPR class I (36.93%), Y. pestis CRISPR class II (41.13%), Y. pestis CRISPR class III (21.93%), E. coli CRISPR class II (42.18%), E. coli class III (2.86%) and E. coli class IV (0.33%). It was observed that there was absence of CRISPR class IV in the genomic sequences of Y. pestis strains analyzed. The percentage distribution of exogenous spacers among E. coli CRISPR classes revealed that CRISPR class I showed 65.77% homologous sequence match with plasmids spacers, 51.96% bacteriophages spacers, 68.26% bacterial spacers, and 20.18% unknown target spacers, while CRISPR II had 79.82% homologous sequence match with unknown self-targets spacers, 49% bacteriophages spacers, 35%plasmids and 29.9% from other bacterial spacers available in NCBI databank. E. coli CRISPR class III showed no homologous spacers sequence match with unknown targets and bacteriophages but showed homologous sequence match with plasmid (0.19%) and other bacteria (1.83%).E. coli CRISPR class IV showed absence of homologous spacers matches against bacteriophages spacers from the NCBI databank. The spacer distribution among Y. pestis CRISPR classes revealed that the CRISPR class I showed a highest percentage value of homologous sequence match with 47.62% bacteriophages spacers, 38.7% plasmids, and 38.44% from other bacterial spacers, while the Y. pestis CRISPR class II showed spacers similarity with plasmids (25.45%) and bacteriophages (25.71%) and Y. pestis CRISPR III also showed percentage similarity sequence match with plasmids spacers(35.84%), bacteriophages spacers(26.67%) and 22.06% bacterial spacers available in NCBI databank. However, there was no homologous spacer sequence match contributed by unknown mobile genetic targets in all the Y. pestis CRISPR classes compared with the E. coli CRISPR classes. The evolutionary relationships of 22 representative strains of each bacterium were carefully selected on temporary relationship over a specific period [n < 10 years] and analyzed. The phylogenetic tree of E. coli revealed that 22 E. coli strains showed a common ancestral origin from E. coli BIDMC_74, and the E. coli BIDMC_74 strain was more closely related to E. coli strain IH57218 than E. coli str. HVH 50 and E. coli str. 122262 NODE_1 respectively. Phylogenetic analysis of all 22 Y. pestis showed a close relationship with one another, suggesting a common evolutionary relationship among them. The results obtained from this study give credence to show that the E.coli showed a significant CRISPR diversity than Y. pestis, in terms of its CRISPR class size, spacer’s contents, exogenous homologous sequence matches and phylogenetic relationships among its strains. This characteristic feature showed by E. coli strains could be attributed to increased homologous spacer acquisition from exogenous plasmids, bacteriophages, bacteria, and unknown targeting elements. The findings further suggest that the increased CRISPR diversity observed in the E. coli could be associated with increased exposure of its strains to these exogenous elements than Y. pestis strains due to bacteriophages infection, co-evolution and conjugation with exogenous mobile genetic elements (MGE).